rs6701545

Variant names:

• chr1-159382177-T-C
• rs6701545
• ENST00000431862.1:n.228-17668A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000431862.1(ENSG00000228560):​n.228-17668A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,788 control chromosomes in the GnomAD database, including 8,844 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.34 (8844 hom., cov: 32)
• Consequence: ENSG00000228560 ENST00000431862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 7 publications found

Genes affected

ENSG00000228560 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228560	ENST00000431862.1	n.228-17668A>G		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51248 AN: 151670 Hom.: 8830 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.321

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.338 AC: 51316 AN: 151788 Hom.: 8844 Cov.: 32 AF XY: 0.342 AC XY: 25373 AN XY: 74164

African (AFR) AF: 0.382 AC: 15857 AN: 41460

American (AMR) AF: 0.396 AC: 6036 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 885 AN: 3462

East Asian (EAS) AF: 0.334 AC: 1728 AN: 5166

South Asian (SAS) AF: 0.292 AC: 1404 AN: 4814

European-Finnish (FIN) AF: 0.348 AC: 3669 AN: 10546

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.305 AC: 20649 AN: 67792

Other (OTH) AF: 0.321 AC: 677 AN: 2108

Alfa AF: 0.323 Hom.: 1343

Bravo AF: 0.344

Asia WGS AF: 0.368 AC: 1270 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.39
PhyloP100		0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6701545; hg19: chr1-159351967;